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Nesvilab / PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
http://www.nesvilab.org/PD-Nodes/
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setup PD2.5 nodes #26

Closed yanwang16 closed 2 years ago

yanwang16 commented 2 years ago

This is a dumb question, after downloading MSFragger and Philosopher and unzip them, am I supposed to copy the folder (MSFragger) and file (philosopher) somewhere? PD gave me the error "unable to access jarfile", and the following message: image

huiyinc commented 2 years ago

Hi,

Do you specify the file path of MSFragger.jar when running the MSFragger PD node (as suggested in our tutorial: https://github.com/Nesvilab/PD-Nodes)?

Best,

Huiyin

yanwang16 @.***> 於 2022年1月22日 下午11:20 寫道：



This is a dumb question, after downloading MSFragger and Philosopher and unzip them, am I supposed to copy the folder (MSFragger) and file (philosopher) somewhere? PD gave me the error "unable to access jarfile", and the following message: [image: image] https://user-images.githubusercontent.com/98223707/150644494-fd75dee8-10dd-4c5c-8188-ba2bdb6fd1c2.png

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYAYOO4E4IGP2LNWT3UXLDKTANCNFSM5MSC7EXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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yanwang16 commented 2 years ago

Thanks, Huiyin. I see now that I didn’t go through the entire instructions. It’s working well now.

Best, Yan

From: chuiyin @.> Sent: Sunday, January 23, 2022 9:02 AM To: Nesvilab/PD-Nodes @.> Cc: Wang, Yan (NIH/NIDCR) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/PD-Nodes] setup PD2.5 nodes (Issue #26)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Hi,

Do you specify the file path of MSFragger.jar when running the MSFragger PD node (as suggested in our tutorial: https://github.com/Nesvilab/PD-Nodes)?

Best,

Huiyin

yanwang16 @.<mailto:@.>> 於 2022年1月22日 下午11:20 寫道：



This is a dumb question, after downloading MSFragger and Philosopher and unzip them, am I supposed to copy the folder (MSFragger) and file (philosopher) somewhere? PD gave me the error "unable to access jarfile", and the following message: [image: image] https://user-images.githubusercontent.com/98223707/150644494-fd75dee8-10dd-4c5c-8188-ba2bdb6fd1c2.png

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYAYOO4E4IGP2LNWT3UXLDKTANCNFSM5MSC7EXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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yanwang16 commented 2 years ago

Another question. Is there additional settings if I use multiple search engines? My search with MSFragger alone worked out fine. But when I tried to use MSFragger alone with Sequest HT, Consensus fails at "PSM Grouper".

huiyinc commented 2 years ago

Hi Yan,

Can you please tell me what PSM validator you use?

Best,

Huiyin

yanwang16 @.***> 於 2022年1月26日 週三 上午12:19寫道：

Another question. Is there additional settings if I use multiple search engines? My search with MSFragger alone worked out fine. But when I tried to use MSFragger alone with Sequest HT, Consensus fails at "PSM Grouper".

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021359678, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYVLSCUDCNQCAAQWULUX3EQRANCNFSM5MSC7EXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

huiyinc commented 2 years ago

Also, there should NOT be any decoy sequences in your fasta file.

Huiyin

Chang Hui-Yin @.***> 於 2022年1月26日 週三 下午2:16寫道：

Hi Yan,

Can you please tell me what PSM validator you use?

Best,

Huiyin

yanwang16 @.***> 於 2022年1月26日 週三 上午12:19寫道：

Another question. Is there additional settings if I use multiple search engines? My search with MSFragger alone worked out fine. But when I tried to use MSFragger alone with Sequest HT, Consensus fails at "PSM Grouper".

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021359678, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYVLSCUDCNQCAAQWULUX3EQRANCNFSM5MSC7EXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you commented.Message ID: @.***>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

yanwang16 commented 2 years ago

My database does not have decoy. For PSM validator, I used Philosopher for MSFragger and “fixed value PSM validator for Sequest”. Do I need to use Philosopher for all?

Yan

From: chuiyin @.> Sent: Wednesday, January 26, 2022 2:04 AM To: Nesvilab/PD-Nodes @.> Cc: Wang, Yan (NIH/NIDCR) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/PD-Nodes] setup PD2.5 nodes (Issue #26)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Also, there should NOT be any decoy sequences in your fasta file.

Huiyin

Chang Hui-Yin @.<mailto:@.>> 於 2022年1月26日 週三 下午2:16寫道：

Hi Yan,

Can you please tell me what PSM validator you use?

Best,

Huiyin

yanwang16 @.<mailto:@.>> 於 2022年1月26日 週三 上午12:19寫道：

Another question. Is there additional settings if I use multiple search engines? My search with MSFragger alone worked out fine. But when I tried to use MSFragger alone with Sequest HT, Consensus fails at "PSM Grouper".

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021359678, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAYVLSCUDCNQCAAQWULUX3EQRANCNFSM5MSC7EXQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you commented.Message ID: @.<mailto:@.>>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021922498, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AXNMMW5UAKIYQVCWGZKMUILUX6MGZANCNFSM5MSC7EXQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you authored the thread.Message ID: @.**@.>>

huiyinc commented 2 years ago

Hi Yan,

PeptideProphet can only be used for MSFragger. I am not sure if it is OK to use multiple PSM validators in the search, because they have different algorithms and the criteria (threshold) might be different. I have performed some analyses using MSFragger and SequestHT coupled with Percolator and the result looks good. So, I would suggest to use Percolator.

Best,

Huiyin

yanwang16 @.***> 於 2022年1月26日 下午9:48 寫道：



My database does not have decoy. For PSM validator, I used Philosopher for MSFragger and “fixed value PSM validator for Sequest”. Do I need to use Philosopher for all?

Yan

From: chuiyin @.> Sent: Wednesday, January 26, 2022 2:04 AM To: Nesvilab/PD-Nodes @.> Cc: Wang, Yan (NIH/NIDCR) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/PD-Nodes] setup PD2.5 nodes (Issue #26)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Also, there should NOT be any decoy sequences in your fasta file.

Huiyin

Chang Hui-Yin @.<mailto:@.>> 於 2022年1月26日 週三 下午2:16寫道：

Hi Yan,

Can you please tell me what PSM validator you use?

Best,

Huiyin

yanwang16 @.<mailto:@.>> 於 2022年1月26日 週三 上午12:19寫道：

Another question. Is there additional settings if I use multiple search engines? My search with MSFragger alone worked out fine. But when I tried to use MSFragger alone with Sequest HT, Consensus fails at "PSM Grouper".

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021359678,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALAWWAYVLSCUDCNQCAAQWULUX3EQRANCNFSM5MSC7EXQ>

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You are receiving this because you commented.Message ID: @.<mailto:@.>>

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

— Reply to this email directly, view it on GitHub< https://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021922498>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AXNMMW5UAKIYQVCWGZKMUILUX6MGZANCNFSM5MSC7EXQ>.

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yanwang16 commented 2 years ago

Hi Huiyin,

Thanks for the suggestions. Yes Percolator worked.

Yan

From: chuiyin @.> Sent: Thursday, January 27, 2022 3:56 AM To: Nesvilab/PD-Nodes @.> Cc: Wang, Yan (NIH/NIDCR) [E] @.>; Author @.> Subject: [EXTERNAL] Re: [Nesvilab/PD-Nodes] setup PD2.5 nodes (Issue #26)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Hi Yan,

PeptideProphet can only be used for MSFragger. I am not sure if it is OK to use multiple PSM validators in the search, because they have different algorithms and the criteria (threshold) might be different. I have performed some analyses using MSFragger and SequestHT coupled with Percolator and the result looks good. So, I would suggest to use Percolator.

Best,

Huiyin

yanwang16 @.<mailto:@.>> 於 2022年1月26日 下午9:48 寫道：



My database does not have decoy. For PSM validator, I used Philosopher for MSFragger and “fixed value PSM validator for Sequest”. Do I need to use Philosopher for all?

Yan

From: chuiyin @.<mailto:@.>> Sent: Wednesday, January 26, 2022 2:04 AM To: Nesvilab/PD-Nodes @.<mailto:@.>> Cc: Wang, Yan (NIH/NIDCR) [E] @.<mailto:@.>>; Author @.<mailto:@.>> Subject: [EXTERNAL] Re: [Nesvilab/PD-Nodes] setup PD2.5 nodes (Issue #26)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

Also, there should NOT be any decoy sequences in your fasta file.

Huiyin

Chang Hui-Yin @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> 於 2022年1月26日 週三 下午2:16寫道：

Hi Yan,

Can you please tell me what PSM validator you use?

Best,

Huiyin

yanwang16 @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> 於 2022年1月26日 週三 上午12:19寫道：

Another question. Is there additional settings if I use multiple search engines? My search with MSFragger alone worked out fine. But when I tried to use MSFragger alone with Sequest HT, Consensus fails at "PSM Grouper".

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/26#issuecomment-1021359678,

or unsubscribe < https://github.com/notifications/unsubscribe-auth/ALAWWAYVLSCUDCNQCAAQWULUX3EQRANCNFSM5MSC7EXQ>

. Triage notifications on the go with GitHub Mobile for iOS < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>

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You are receiving this because you commented.Message ID: @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

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